The purpose of this Shiny application is to interactively and quickly review previously found genetic Inflammatory Bowel Disease associations identified by the Cedars-Sinai F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute.
Users can search associations by Gene (e.g. NOD2), Position (e.g. Chr. 16, between 50731050-50766987), SNP (e.g. rs5743293 or imm_2_204278337), or by File of either a list of genes or SNPs. Searching by position queries by the position of the SNP not by the position of the Gene.
Users can search by multiple Genes or SNPs at a time by selecting multiple Genes or SNPs respectively. If a user has a large list of Genes or SNPs they can copy and paste them into the search box but the Genes/SNPs must be in comma separated format (e.g. IL1,IL2,IL3,IL4,IL5,IL6,IL7,IL8,IL9,IL10,IL11). Due to the large marker list it is possible that your SNP or gene might not be loaded into memory. Typing your SNP out manually will ensure it is correctly visualized.
If you are going to upload a list of Genes or SNPs, the file must consist of a single column of Genes or SNPs in a standard format. The column can be named or un-named.
Users can filter their query to only include SNP associations that reach user defined thresholds. Users can filter by:
- P Value
- Minor Allele Frequency (in the future)
- SNP Location (e.g. intron, coding, complex...)
- Overall Missingness (in the future)
- Overall Hardy-Weinberg Assumptions (in the future)
Once a table of results is returned, a user can sub-filter the table by the output to further narrow down the results.
For users who are interested in downloading their query, a Download button can be found at the bottom of every table. The downloaded data will reflect the filters applied from the query, but the "sub-filters" will not be applied.
In total, 68 unique phenotypes generated by 5 analysts are deposited into this repository (2018-06-11). Please contact the analyst listed if you have any additional questions about the significance of their result.
In cases when permutation was performed, the permuted P value replaces the queryable P value and the original (non-permutted) P value is displayed next to the permutted value on he Gene-Pheno-SNP tab.
Markers have been annotated with cis-eQTL data from the Cedars-Sinai Small Bowel 139 dataset. If the relevant loci is also a cis-eQTL in the small bowel dataset, the relevant eGENE, betas and p vaues are also listed next to the marker on the Geno-Pheno-SNP tab. Markers are designated as priority if the eQTL is positioned inside the eGENE or is flanked by the eGENE. eQTL corresponding to insertions and deletions are not included in the application.
| Analyst | PHENOTYPE | Population | Notes | Year |
|---|---|---|---|---|
| Alka | A_Spondylitis | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | A_Spondylitis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Arthralgias | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Arthralgias | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | B1 | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | B2 | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | B3 | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Crohn's Disease vs. non-IBD Controls | Crohn's Disease | Case-control with ichip1-5 and DX 2016 phenotype file from Linda and using 75% Caucasian independent. Covariates including first 4 PCs | 2016 - 2017 |
| Alka | E_Nodosum | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | E_Nodosum | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | IBD vs. non-IBD Controls | IBD | Case-control with ichip1-5 and DX 2016 phenotype file from Linda and using 75% Caucasian independent. Covariates including first 4 PCs | 2016 - 2017 |
| Alka | Iritis | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Iritis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | L1_ileal | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | L2_colonic | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | L3_ileocolonic | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | L4_UpperGIDisease | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | LeftSided | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | OralUlcers | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Pancolitis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | PDM | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Proctitis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | PSC | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Psoriasis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | PyodermaG | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | PyodermaG | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Smoking_Status | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Smokinghx | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Surgery | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Surgery | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Thrombosis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Time to Frist Surgery | Crohn's Disease | Time to first CD surgery associations with ichip1-5 and Sultan’s phenotype file and using 75% Caucasian independent samples. For second surgery, phenotype file from DM. Covariates include first 4 PCs | 2016 - 2017 |
| Alka | Time to Second Surgery | Crohn's Disease | Time to Second CD surgery associations with ichip1-5 and Sultan’s phenotype file and using 75% Caucasian independent samples. For second surgery, phenotype file from DM. Covariates include first 4 PCs | 2016 - 2017 |
| Alka | Ulcerative Colitis vs. non-IBD Controls | Ulcerative Colitis | Case-control with ichip1-5 and DX 2016 phenotype file from Linda and using 75% Caucasian independent. Covariates including first 4 PCs | 2016 - 2017 |
| Alka | Uveitis | Crohn's Disease | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Alka | Uveitis | Ulcerative Colitis | 75% Caucasian independent samples, phenotypes from Sultan's File, ichip 1-5 | 2016 - 2017 |
| Dalin | Anca CD vs. Anca Ctrl | Crohn's Disease | iChip | 2017 |
| Dalin | Anca UC vs. Anca Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | Asca CD vs. Asca Ctrl | Crohn's Disease | iChip | 2017 |
| Dalin | Asca UC vs. Asca Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | Cbir CD vs. Cbir Ctrl | Crohn's Disease | iChip | 2017 |
| Dalin | Cbir UC vs. Cbir Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | CD vs. Ctrl | Crohn's Disease | Meta of Cedars, IIBDGC, De Lange paper cohorts | 2018 |
| Dalin | i2 CD vs. i2 Ctrl | Crohn's Disease | iChip | 2017 |
| Dalin | i2 UC vs. i2 Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | IBD vs. Ctrl | IBD | Meta of Cedars, IIBDGC, De Lange paper cohorts | 2018 |
| Dalin | IGA Asca UC vs. IGA Asca Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | IGG Asca CD vs. IGA Asca Ctrl | Crohn's Disease | iChip | 2017 |
| Dalin | IGG Asca UC vs. IGA Asca Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | OMPC CD vs. OMPC Ctrl | Crohn's Disease | iChip | 2017 |
| Dalin | OMPC UC vs. OMPC Ctrl | Ulcerative Colitis | iChip | 2017 |
| Dalin | UC vs. Ctrl | Ulcerative Colitis | Meta of Cedars, IIBDGC, De Lange paper cohorts | 2018 |
| Marcy | Perianal CD+ vs. Perianal CD- | Crohn's Disease | International Cohort | 2018 |
| Shishir | L1 B1 vs non-IBD ctrl | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L1 B2a+B2b vs B1 | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L1 B2a+B2b vs non-IBD ctrl | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L2 B1 vs non-IBD ctrl | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L2 B2a+B2b vs B1 | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L2 B2a+B2b vs non-IBD ctrl | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L3 B1 vs non-IBD ctrl | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L3 B2a+B2b vs B1 | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Shishir | L3 B2a+B2b vs non-IBD ctrl | Crohn's Disease | iChip 1-7, Caucasian | 2018 |
| Talin | anti-TNF primary non-response vs primary response | Crohn's Disease | Cedars ichip1-5 CD anti-TNF all races but mostly Caucasian, adjusted for 2PC, smoking, disease location, combination therapy | 2015 - 2016 |
| Talin | anti-TNF primary non-response vs primary response | IBD | Cedars ichip1-5 all IBD anti-TNF all races but mostly Caucasian, adjusted for 2PC, age dx | 2015 - 2016 |
| Talin | anti-TNF primary non-response vs primary response | Ulcerative Colitits | Cedars ichip1-5 UC anti-TNF all races but mostly Caucasian, adjusted for 2PC | 2015 - 2016 |
| Talin | anti-TNF time to loss of response | Crohn's Disease | Cedars ichip1-5 CD anti-TNF all races but mostly Caucasian, adjusted for 2PC, anca level, family history IBD | 2015 - 2016 |
| Talin | anti-TNF time to loss of response | IBD | Cedars ichip1-5 all IBD anti-TNF all races but mostly Caucasian, adjusted for 2PC, fam dx | 2015 - 2016 |
| Talin | anti-TNF time to loss of response | Ulcerative Colitits | Cedars ichip1-5 UC anti-TNF all races but mostly Caucasian, adjusted for 2PC, ompc positivity, anca positivity | 2015 - 2016 |
| Talin | MRUC time to colectomy | Ulcerative Colitis | Meta-analysis of Cedars iChip1-4 and international IIBDGC ichip using SNP2HLA (MHC/HLA) imputed, Caucasian only | 2015 - 2016 |
| Talin | MRUC time to colectomy | Ulcerative Colitis | Meta-analysis of Cedars iChip1-4 and international IIBDGC ichip, Caucasian only | 2015 - 2016 |
| Talin | MRUC Time to Colectomy <60 months vs >60 months | Ulcerative Colitis | Meta-analysis of Cedars iChip1-4 and international IIBDGC ichip using SNP2HLA (MHC/HLA) imputed, Caucasian only | 2015 - 2016 |
| Talin | MRUC Time to Colectomy <60 months vs >60 months | Ulcerative Colitis | Meta-analysis of Cedars iChip1-4 and international IIBDGC ichip, Caucasian only | 2015 - 2016 |
| Talin | MRUC vs non-MRUC | Ulcerative Colitis | Meta-analysis of Cedars iChip1-4 and international IIBDGC ichip using SNP2HLA (MHC/HLA) imputed, Caucasian only | 2015 - 2016 |
| Talin | MRUC vs non-MRUC | Ulcerative Colitis | Meta-analysis of Cedars ichip1-4 and international IIBDGC ichip, Caucasian only | 2015 - 2016 |
| Talin | Paneth high (>20%) vs low (<20%) abnormal paneth phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC | 2016 - 2017 |
| Talin | Paneth-D0 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
| Talin | Paneth-D1 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
| Talin | Paneth-D1234 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
| Talin | Paneth-D2 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
| Talin | Paneth-D3 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
| Talin | Paneth-D4 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
| Talin | Paneth-D5 phenotype | Crohn's Disease | Cedars ichip1-6 + Stappenbeck samples, Caucasian only, adjusted for 2PC; with corresponding permuted results for selected top snps [permuted due to highly skewed phenotype; need EMP1 pvalues from permuted | 2016 - 2017 |
The backbone of the application is genetic association tests performed by scientists at the Cedars-Sinai Inflammatory Bowel and Immunobiology Research Institute. To have your association stored in this application the following information is needed in a CSV file per association performed.
- Illumina Chip ID
- P Value
- Odds Ratio or B Value
- Confidence Intervals (if performed)
- The number of patients in the association (total number in association, both cases and controls)
- A1
In addition to the above the analyst will need to submit information on:
- The name of the analyst who performed the association
- The year the analysis was run
- The sample of patients the association was performed on (e.g. Disease Sub-Type (CD or UC), Race, Ethnicity, Jewish, other unique criteria of your analysis)
- The phenotype tested
All annotation data was produced by Alka Potdar, PhD and correspond to hg19 genomic locations. The following annovar databases were used dbSNP = avsnp147, UCSC knownGene (Gene in the application) and Functional location, and NCBI RefGene.
Hardy-Weinberg, minor allele frequency, and missingness will be performed globally yet might not be applicable to all sub-populations studied.
For markers without an assigned known functional location, they have been assigned UNK. For markers withut an assigned chromosome they have been asigned Chr 999. For markers without an assigned SNP base pair location, they have been assigned location 0 on the corresponding chromosome.
The Cedars-Sinai F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute Translational Genomics Group.